# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 15:42:08 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: (1R,5R,8R,9aS)-1,9a-dimethyl-8-(prop-1-en-2-yl)octahydro-2H-quinolizinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CCC[NH+]2CC[C@H](C[C@@]12C)C(C)=C
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 JF2  JF2  (1R,5R,8R,9aS)-1,9a-dimethyl-8-(prop-1-en-2-yl)octahydro-2H-quinolizinium  ligand  41  15  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_JF2
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 JF2  CAJ  C  CH2   0  -0.429  -0.7273   0.7470   0.1401
 JF2  CAO  C  CT    0   0.078   0.6973   0.3665  -0.2789
 JF2  CAD  C  CH3   0  -0.698   0.8677   0.4489  -1.7907
 JF2  CAM  C  CH1   0  -0.236   1.7293   1.2394   0.4743
 JF2  CAC  C  CH3   0  -0.670   1.6204   2.7182   0.1167
 JF2  CAF  C  CH2   0  -0.433   3.1619   0.7504   0.2673
 JF2  CAE  C  CH2   0  -0.469   3.3196  -0.7118   0.6504
 JF2  CAH  C  CH2   0  -0.311   2.3035  -1.5828  -0.0538
 JF2  NAN  N  NT1   1  -0.544   0.9218  -1.0735   0.1972
 JF2  CAI  C  CH2   0  -0.315  -0.1007  -2.0434  -0.2990
 JF2  CAG  C  CH2   0  -0.455  -1.4961  -1.6181   0.1004
 JF2  CAL  C  CH1   0  -0.343  -1.8078  -0.2020  -0.3819
 JF2  CAK  C  C     0   0.209  -3.1920   0.2484   0.0208
 JF2  CAB  C  C2    0  -0.597  -4.1144   0.4945  -0.9073
 JF2  CAA  C  CH3   0  -0.739  -3.4848   0.4093   1.4843
 JF2  H1   H  HCH2  0   0.255  -0.7697   0.7932   1.2342
 JF2  H2   H  HCH2  0   0.277  -0.9249   1.7569  -0.2200
 JF2  H3   H  HCH3  0   0.263   0.2297  -0.2469  -2.3316
 JF2  H4   H  HCH3  0   0.274   0.5804   1.4469  -2.1179
 JF2  H5   H  HCH3  0   0.263   1.8923   0.2850  -2.1187
 JF2  H6   H  HCH1  0   0.247   1.4970   1.1419   1.5440
 JF2  H7   H  HCH3  0   0.245   0.6307   3.1291   0.3104
 JF2  H8   H  HCH3  0   0.248   2.3290   3.2860   0.7197
 JF2  H9   H  HCH3  0   0.232   1.8670   2.8994  -0.9297
 JF2  H10  H  HCH2  0   0.235   3.4690   0.9035  -0.7714
 JF2  H11  H  HCH2  0   0.258   3.8305   1.3611   0.8763
 JF2  H12  H  HCH2  0   0.273   4.3149  -1.0786   0.3968
 JF2  H13  H  HCH2  0   0.249   3.2082  -0.8317   1.7321
 JF2  H14  H  HCH2  0   0.292   2.4547  -1.6137  -1.1315
 JF2  H15  H  HCH2  0   0.303   2.3316  -2.6062   0.3166
 JF2  H16  H  HNT1  0   0.447   0.8125  -1.0483   1.2153
 JF2  H17  H  HCH2  0   0.292   0.0148  -2.1277  -1.3783
 JF2  H18  H  HCH2  0   0.308   0.1529  -3.0073   0.1386
 JF2  H19  H  HCH2  0   0.278  -2.1998  -2.3364  -0.3228
 JF2  H20  H  HCH2  0   0.251  -1.5915  -1.6826   1.1884
 JF2  H21  H  HCH1  0   0.259  -1.7741  -0.2020  -1.4756
 JF2  H22  H  H     0   0.233  -5.1156   0.8135  -0.6442
 JF2  H23  H  H     0   0.234  -3.9000   0.3873  -1.9639
 JF2  H24  H  HCH3  0   0.245  -2.8699   1.1931   1.9319
 JF2  H25  H  HCH3  0   0.249  -4.5277   0.6743   1.6514
 JF2  H26  H  HCH3  0   0.242  -3.2790  -0.5049   2.0449

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 JF2  CAF  CAE  single  1.520  0.020  1.520
 JF2  CAF  CAM  single  1.528  0.020  1.528
 JF2  CAC  CAM  single  1.525  0.020  1.525
 JF2  CAE  CAH  single  1.512  0.020  1.512
 JF2  CAM  CAO  single  1.547  0.020  1.547
 JF2  CAH  NAN  single  1.494  0.020  1.494
 JF2  CAO  CAD  single  1.524  0.020  1.524
 JF2  CAO  NAN  single  1.533  0.020  1.533
 JF2  CAO  CAJ  single  1.533  0.020  1.533
 JF2  NAN  CAI  single  1.494  0.020  1.494
 JF2  CAJ  CAL  single  1.530  0.020  1.530
 JF2  CAI  CAG  single  1.513  0.020  1.513
 JF2  CAL  CAG  single  1.528  0.020  1.528
 JF2  CAL  CAK  single  1.510  0.020  1.510
 JF2  CAA  CAK  single  1.501  0.020  1.501
 JF2  CAK  CAB  double  1.331  0.020  1.331
 JF2  CAJ  H1   single  0.970  0.020  1.090
 JF2  CAJ  H2   single  0.970  0.020  1.090
 JF2  CAD  H3   single  0.970  0.020  1.090
 JF2  CAD  H4   single  0.970  0.020  1.090
 JF2  CAD  H5   single  0.970  0.020  1.090
 JF2  CAM  H6   single  0.970  0.020  1.090
 JF2  CAC  H7   single  0.970  0.020  1.090
 JF2  CAC  H8   single  0.970  0.020  1.090
 JF2  CAC  H9   single  0.970  0.020  1.090
 JF2  CAF  H10  single  0.970  0.020  1.090
 JF2  CAF  H11  single  0.970  0.020  1.090
 JF2  CAE  H12  single  0.970  0.020  1.090
 JF2  CAE  H13  single  0.970  0.020  1.090
 JF2  CAH  H14  single  0.970  0.020  1.090
 JF2  CAH  H15  single  0.970  0.020  1.090
 JF2  NAN  H16  single  0.890  0.020  1.040
 JF2  CAI  H17  single  0.970  0.020  1.090
 JF2  CAI  H18  single  0.970  0.020  1.090
 JF2  CAG  H19  single  0.970  0.020  1.090
 JF2  CAG  H20  single  0.970  0.020  1.090
 JF2  CAL  H21  single  0.970  0.020  1.090
 JF2  CAB  H22  single  0.930  0.020  1.080
 JF2  CAB  H23  single  0.930  0.020  1.080
 JF2  CAA  H24  single  0.970  0.020  1.090
 JF2  CAA  H25  single  0.970  0.020  1.090
 JF2  CAA  H26  single  0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 JF2  H2   CAJ  H1   106.48  3.000
 JF2  H2   CAJ  CAL  109.51  3.000
 JF2  H1   CAJ  CAL  109.84  3.000
 JF2  H2   CAJ  CAO  107.94  3.000
 JF2  H1   CAJ  CAO  108.62  3.000
 JF2  CAL  CAJ  CAO  114.15  3.000
 JF2  NAN  CAO  CAM  106.32  3.000
 JF2  NAN  CAO  CAD  110.03  3.000
 JF2  CAM  CAO  CAD  112.21  3.000
 JF2  NAN  CAO  CAJ  106.52  3.000
 JF2  CAD  CAO  CAJ  111.21  3.000
 JF2  CAM  CAO  CAJ  110.28  3.000
 JF2  H5   CAD  H4   107.21  3.000
 JF2  H5   CAD  H3   107.82  3.000
 JF2  H4   CAD  H3   106.38  3.000
 JF2  H5   CAD  CAO  113.34  3.000
 JF2  H4   CAD  CAO  108.55  3.000
 JF2  H3   CAD  CAO  113.15  3.000
 JF2  H6   CAM  CAF  107.56  3.000
 JF2  H6   CAM  CAC  107.41  3.000
 JF2  CAF  CAM  CAC  110.21  3.000
 JF2  H6   CAM  CAO  106.43  3.000
 JF2  CAC  CAM  CAO  112.65  3.000
 JF2  CAF  CAM  CAO  112.26  3.000
 JF2  H9   CAC  H8   107.30  3.000
 JF2  H9   CAC  H7   108.27  3.000
 JF2  H8   CAC  H7   107.21  3.000
 JF2  H9   CAC  CAM  111.72  3.000
 JF2  H8   CAC  CAM  109.20  3.000
 JF2  H7   CAC  CAM  112.89  3.000
 JF2  H11  CAF  H10  106.23  3.000
 JF2  H11  CAF  CAE  109.52  3.000
 JF2  H10  CAF  CAE  110.17  3.000
 JF2  H11  CAF  CAM  108.65  3.000
 JF2  H10  CAF  CAM  110.31  3.000
 JF2  CAE  CAF  CAM  111.78  3.000
 JF2  H13  CAE  H12  106.62  3.000
 JF2  H13  CAE  CAH  109.20  3.000
 JF2  H12  CAE  CAH  108.13  3.000
 JF2  H13  CAE  CAF  110.13  3.000
 JF2  H12  CAE  CAF  111.08  3.000
 JF2  CAH  CAE  CAF  111.53  3.000
 JF2  H15  CAH  H14  107.85  3.000
 JF2  H15  CAH  NAN  106.69  3.000
 JF2  H14  CAH  NAN  107.73  3.000
 JF2  H15  CAH  CAE  111.44  3.000
 JF2  H14  CAH  CAE  112.58  3.000
 JF2  NAN  CAH  CAE  110.30  3.000
 JF2  H16  NAN  CAI  105.85  3.000
 JF2  H16  NAN  CAH  105.90  3.000
 JF2  CAI  NAN  CAH  110.84  3.000
 JF2  H16  NAN  CAO  105.67  3.000
 JF2  CAI  NAN  CAO  113.98  3.000
 JF2  CAH  NAN  CAO  113.79  3.000
 JF2  H18  CAI  H17  107.78  3.000
 JF2  H18  CAI  CAG  110.97  3.000
 JF2  H17  CAI  CAG  112.42  3.000
 JF2  H18  CAI  NAN  106.37  3.000
 JF2  H17  CAI  NAN  107.87  3.000
 JF2  CAG  CAI  NAN  111.16  3.000
 JF2  H20  CAG  H19  106.90  3.000
 JF2  H20  CAG  CAL  110.53  3.000
 JF2  H19  CAG  CAL  110.86  3.000
 JF2  H20  CAG  CAI  109.06  3.000
 JF2  H19  CAG  CAI  107.90  3.000
 JF2  CAL  CAG  CAI  111.43  3.000
 JF2  H21  CAL  CAK  107.14  3.000
 JF2  H21  CAL  CAG  108.01  3.000
 JF2  CAK  CAL  CAG  112.28  3.000
 JF2  H21  CAL  CAJ  108.62  3.000
 JF2  CAK  CAL  CAJ  111.79  3.000
 JF2  CAG  CAL  CAJ  108.85  3.000
 JF2  CAA  CAK  CAB  121.64  3.000
 JF2  CAB  CAK  CAL  120.28  3.000
 JF2  CAA  CAK  CAL  118.08  3.000
 JF2  H23  CAB  H22  116.67  3.000
 JF2  H23  CAB  CAK  121.63  3.000
 JF2  H22  CAB  CAK  121.70  3.000
 JF2  H26  CAA  H25  107.79  3.000
 JF2  H26  CAA  H24  106.52  3.000
 JF2  H25  CAA  H24  107.56  3.000
 JF2  H26  CAA  CAK  111.96  3.000
 JF2  H25  CAA  CAK  111.25  3.000
 JF2  H24  CAA  CAK  111.51  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 JF2  Var_01  CAH  CAE  CAF  CAM   53.09  30.0  1
 JF2  Var_02  NAN  CAH  CAE  CAF  -54.31  30.0  1
 JF2  Var_03  CAL  CAG  CAI  NAN   55.70  30.0  1
 JF2  Var_04  H22  CAB  CAK  CAL  179.67   0.0  2
 JF2  Var_05  H24  CAA  CAK  CAL   63.58  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 JF2  chir_01  CAO  CAM  NAN  CAJ  negativ
 JF2  chir_02  CAM  CAO  CAC  CAF  positiv
 JF2  chir_03  NAN  CAI  CAO  CAH  positiv
 JF2  chir_04  CAL  CAJ  CAG  CAK  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 JF2  plan-1  CAL  0.020
 JF2  plan-1  CAK  0.020
 JF2  plan-1  CAB  0.020
 JF2  plan-1  CAA  0.020
 JF2  plan-1  H22  0.020
 JF2  plan-1  H23  0.020

